TOKYO—Negligence by the Japanese government and Tokyo Electric Power Co. caused the triple meltdowns at the Fukushima Daiichi nuclear power plant, a court ruled Tuesday in the biggest class-action suit related to the March 2011 accident.

The Fukushima District Court on Tuesday ordered the government and Tepco to pay a total of ¥498 million ($4.4 million) plus delinquency charges to 2,907 people who fled the radiation that was released into the air and water after a tsunami flooded the power plant, knocking out the power to…